Describe the numerical abundance of microbial life in relation to ecology and biogeochemistry of Earth systems.
Comment on the emergence of microbial life and the evolution of Earth systems
Indicate the key events in the evolution of Earth systems at each approximate moment in the time series. If times need to be adjusted or added to the timeline to fully account for the development of Earth systems, please do so.
Describe the dominant physical and chemical characteristics of Earth systems at the following waypoints:
Evaluate human impacts on the ecology and biogeochemistry of Earth systems.
What were the main questions being asked?
Describe the numerical abundance of microbial life in relation to the ecology and biogeochemistry of Earth systems.
| Primary Habitats | Total Cell Abundance |
|---|---|
| Open ocean | \(1.2*10^{29}\) |
| Soil | \(2.6*10^{29}\) |
| Subsurface | \(3.8*10^{30}\) |
| Oceanic subsurface | \(3.5*10^{30}\) |
| Terrestrial subsurface | \(0.25*10^{30}\) to \(2.3*10^{30}\) |
What is the estimated prokaryotic cell abundance in the upper 200 m of the ocean and what fraction of this biomass is represented by marine cyanobacterium including Prochlorococcus? What is the significance of this ratio with respect to carbon cycling in the ocean and the atmospheric composition of the Earth?
What is the difference between an autotroph, heterotroph, and a lithotroph based on information provided in the text?
Autotroph – “self-nourishing” – uses inorganic carbon to produce complex organic carbon as a source of carbon for other organotrophs (fixing CO2 into biomass).
Heterotroph – uses organic carbon assimilated by autotrophs as sources of carbon. Assimilate organic carbon.
Lithotroph – technically obtains electron sources from inorganic chemicals, they can use material other than inorganic carbon to obtain reducing agents. Use inorganic substrates.
Based on information provided in the text and your knowledge of geography what is the deepest habitat capable of supporting prokaryotic life? What is the primary limiting factor at this depth?
Based on information provided in the text your knowledge of geography what is the highest habitat capable of supporting prokaryotic life? What is the primary limiting factor at this height?
Based on estimates of prokaryotic habitat limitation, what is the vertical distance of the Earth’s biosphere measured in km?
How was annual cellular production of prokaryotes described in Table 7 column four determined? (Provide an example of the calculation)
What is the relationship between carbon content, carbon assimilation efficiency and turnover rates in the upper 200m of the ocean? Why does this vary with depth in the ocean and between terrestrial and marine habitats?
How were the frequency numbers for four simultaneous mutations in shared genes determined for marine heterotrophs and marine autotrophs given an average mutation rate of 4 x 10-7 per DNA replication? (Provide an example of the calculation with units. Hint: cell and generation cancel out)
Given the large population size and high mutation rate of prokaryotic cells, what are the implications with respect to genetic diversity and adaptive potential? Are point mutations the only way in which microbial genomes diversify and adapt?
Discuss the role of microbial diversity and formation of coupled metabolism in driving global biogeochemical cycles.
What are the primary geophysical and biogeochemical processes that create and sustain conditions for life on Earth? How do abiotic versus biotic processes vary with respect to matter and energy transformation and how are they interconnected?
Why is Earth’s redox state considered an emergent property?
What is the relationship between microbial diversity and metabolic diversity and how does this relate to the discovery of new protein families from microbial community genomes?
On what basis do the authors consider microbes the guardians of metabolism?
“Microbial life can easily live without us; we, however, cannot survive without the global catalysis and environmental transformations it provides.” Do you agree or disagree with this statement? Answer the question using specific reference to your reading, discussions and content from evidence worksheets and problem sets
For billions of years, microbial life drove the establishment of Earth’s biogeochemical cycles and coevolved with ancestors that ultimately lead to the evolution of Homo sapiens. But does the future of our planet lie solely in the hands of humans, while microbes are merely a remnant of the past? Ultimately, humans have been reliant on microbes and will continue to depend on them to ensure survival of our species in the following three ways. Firstly, microbes being an essential part of Earth’s biogeochemical cycles have established the Earth suitable for human survival. Secondly, human industrialization has rapidly expanded technologies that can rival certain microbial processes in a large scale, but in an unbalanced manner that has resulted in biogeochemical cycle disruptions. Lastly, humans must eventually rely on microbial metabolism to re-establish a balanced biogeochemical system. Humans live in a world that would not have existed without microbes, but microbes can easily continue to thrive without humans.
Microbial influence on altering Earth’s atmosphere and biogeochemical landscapes
Microbial life has intimately provided metabolic processes that drives Earth’s atmosphere and geochemical landscape for the survival of humans. The earliest evidence of microbial activity was present at least 3.5 billion years ago (Gya) (1), derived from stable carbon-isotope and sulfur-isotope fractionation that suggested possible sulfate reduction and methanogenesis (2). Along with volcanic release of mantle gasses, these methanogenic bacteria have in part contributed to an anoxic early earth atmosphere rich in carbon dioxide and methane (2). The greenhouse-effect from atmospheric methane was speculated to have prevented a glacial Earth under the faint young sun, with only one third of solar radiation than the modern sun (3). Even in our modern atmosphere, micro-organisms such as methanogens continue to contribute to the trace gases, whose sources are almost entirely biological (4). Approximately 2.45 Gya, oxygenic photosynthesis performed by Cyanobacteria lead to an initial rise in atmospheric oxygen. Specifically, the removal of carbon from the buried organic matter in sediments by oxygenic phototrophy produced oxygen, which cannot re-enter the marine carbon cycle and thus remained in the atmosphere (4). These microbes produced rapid rise of atmospheric oxygen as by-products, and lead to the Great Oxidation Event (1). The rapidly rising reactive oxygen species in the oxygenated atmosphere were toxic to most anaerobes, and resulted in mass extinction of anaerobic niches (3). This selective pressure aided the widespread establishment of aerobic microorganisms, and ultimately paved way for the evolution of complex organisms today. The microbial catalysis of geochemical processes as a by-product of their metabolism have played an important role in shaping the environment in which we currently live in.
Industrial replacement of microbial processes lead to disruptions of biogeochemical cycle
The rapidly increasing human population and technological leaps have triggered a new Anthropocene landscape that requires constant management to maintain ecological balance, one that we have a difficult time keeping up. An example of this is the Haber-Bosch process for industrial nitrogen fixation. Humans are capable of replacing microbial metabolism with nitrogen fixation that is twice the natural nitrogen cycle (5). However, the Haber-Bosch process has resulted in a disproportional input of nitrogen that not only impacts the nitrogen cycle, but also affects other natural cycles of chemical elements. The distortion of basic biogeochemical cycles across the globe is a result of the decoupling of intimate interactions between the natural cycles (6). For example, the high input of industrially synthesized ammonia in fertilizers can be converted by nitrifying bacteria into the highly mobile nitrate, which leaches into aquatic ecosystems. The overabundance of nitrogen in this ecosystem positively feeds-forward the carbon cycle by increasing organic carbon, which removes oxygen during decomposition (7). This results in hypoxic zones around the world and creates huge loss of aquatic biodiversity (7). Ultimately, disruption in the interdependence of natural cycles will eventually require constant human intervention to maintain biogeochemical balance (6). The advent of industrial processes that carry out microbial metabolism has resulted in the disruption of natural biogeochemical cycles, humans are limited as interventionalists in dictating the future of our planet without microbes.
The role of microbes in biogeochemical cycles as a solution to environmental disruptions
The industrial processes implemented to supplement microbial metabolism have wrecked havoc on the natural biogeochemical cycles, and humans must turn to microbes to re-establish a balanced biogeochemical system. Despite earlier mentions of human industrial processes, microbes today continue to support human sustainability through reduction-oxidation (redox) reactions. They work with abiotic processes to maintain the balance of the six major bio-elements, hydrogen (H), carbon (C), nitrogen (N), oxygen (O), sulfur (S) and phosphorus (P) (2). Of all the biogeochemical cycles, the nitrogen cycle is the only one that is entirely biologically driven (2). The biological N cycle is balanced by five different reactions - nitrogen fixation, nitrification, anammox, denitrification and ammonification, which are all maintained by the synergistic cooperation of multiple microbes (8). Without human intervention, nitrogen fixation is the only biological process that converts N2 into ammonium (NH4+), which is carried out by certain microbes expressing enzyme nitrogenase. In agriculture, legume plants form symbiotic associations with some nitrogen-fixing species of Rhizobium, for accessible forms of N used in proteins and nucleic acids synthesis (8). NH4+ can be oxidized back into nitrate in a two-step nitrification pathway, then denitrification converts the product into N2 to complete the nitrogen cycle (8). As nitrogenase is highly sensitive to oxygen, each step of the cycle is catalyzed by specific group of bacteria in the presence of oxygen, and they work synergistically to maintain balance in the input and output of global nitrogen resources (2). Modern agriculture is a major case of environmental pollution, there is a need for more sustainable solutions to nitrogen fertilizer use. Humans have used techniques such as intercropping and crop rotation to help naturally increase nitrogen content of the soil, but these methods are time consuming (8). Scientists are now looking at biological engineering to introduce nitrogen-fixing microbial metabolism to non-legume crops, in order to reduce the requirement for exogenous fertilization (9). Currently there are two strategic approaches in non-legume plants: investigation of non-legume nitrogen-fixing bacteria, and genetic engineering of signalling pathway to create a rhizobium-friendly environment in the plant nodules (9). With biological nitrogen sources, microbes can balance the natural feedback system in a more constrained manner, to produce a new steady state of the N cycle over time (3). Thus, microbes have not only improved human quality of life, they may also be the solution to ensure planetary and human sustainability.
Conclusion
Microbes play an essential role in driving important biogeochemical cycles that ultimately developed into a suitable environment for human survival in the past, present and future. The global catalysis as a result of photosynthetic metabolic by-products helped established an oxygenated environment appropriate for human evolution. However, humans’ lack of understanding on the consequences of our current actions have lead to imbalances in biogeochemical cycles. With more understanding of microbial metabolism, the pathways may be used for renewable sources of materials, and has the potential to save the Earth from the destructions created by our ignorance. In this sense, humans must continue to explore for a complete picture of microbial metabolic diversity, to ensure self-sustainability in the long run.
Achenbach, J. 2012. Spaceship Earth: A new view of environmentalism. Washington Post (January 2, 2012).Washington Post
Bernhard, A. 2010. The nitrogen cycle: processes. players, and human impact. Nature Education Knowledge. 3:25 Nature Education
Canfield, DE, Glazer, AN, Falkowski, PG. 2010. The evolution and future of Earth’s nitrogen cycle. Science. 330:192-196.PMID20929768
Dent, D, Cocking, E. 2017. Establishing symbiotic nitrogen fixation in cereals and other non-legume crops: The Greener Nitrogen Revolution. Agriculture & Food Security. 6:7.https://doi.org/10.1186/s40066-016-0084-2
Falkowski, PG, Fenchel, T, Delong, EF. 2008. The microbial engines that drive Earth’s biogeochemical cycles. Science. 320:1034-1039.PMID20929768
Falkowski, P, Scholes, RJ, Boyle, E, Canadell, J, Canfield, D, Elser, J, Gruber, N, Hibbard, K, Hugberg, P, Linder, S. 2000. The global carbon cycle: a test of our knowledge of earth as a system. Science. 290:291-296.PMID11030643
Fuerst, JA, Sagulenko, E. 2011. Beyond the bacterium: planctomycetes challenge our concepts of microbial structure and function. Nature Reviews Microbiology.9:403.PMID20929768
Gilbert, JA, Neufeld, JD. 2014. Life in a World without Microbes. PLoS Biol. 12:12. PMC4267716
Kallmeyer, J, Pockalny, R, Adhikari, RR, Smith, DC, D’Hondt, S. 2012. Global distribution of microbial abundance and biomass in subseafloor sediment. Proceedings of the National Academy of Sciences. 109:16213-16216.PMID22927371
Kasting, JF, Siefert, JL. 2002. Life and the evolution of Earth’s atmosphere. Science. 296:1066-1068.PMID12004117
Leopold, A. 2014. The land ethic, p. 108-121. In Anonymous The Ecological Design and Planning Reader. Springer.Springer
Mooney, C. 2016. Scientists say humans have now brought on an entirely new geologic epoch. The Washington Post. Article
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The remaining second level headers (##) are for separating data science Friday, regular course, and project content. In this module, you will only need to include data science Friday and regular course content; projects will come later in the course.
Third level headers (###) should be used for links to assignments, evidence worksheets, problem sets, and readings, as seen here.
Use this space to include your installation screenshots.
RStudio
GitHub homepage
Detail the code you used to create, initialize, and push your portfolio repo to GitHub. This will be helpful as you will need to repeat many of these steps to update your porfolio throughout the course.
starting from after registering for a new GitHub account
1. git init
2. git add .
3. git commit -m “First commit”
4. git remote add origin https://github.com/judyban/MICB425_portfolio
5. git remote -v
6. git push -u origin master
Repeat steps 2, 3 and git push to push new materials into the repository
The following assignment is an exercise for the reproduction of this .html document using the RStudio and RMarkdown tools we’ve shown you in class. Hopefully by the end of this, you won’t feel at all the way this poor PhD student does. We’re here to help, and when it comes to R, the internet is a really valuable resource. This open-source program has all kinds of tutorials online.
http://phdcomics.com/ Comic posted 1-17-2018
The goal of this R Markdown html challenge is to give you an opportunity to play with a bunch of different RMarkdown formatting. Consider it a chance to flex your RMarkdown muscles. Your goal is to write your own RMarkdown that rebuilds this html document as close to the original as possible. So, yes, this means you get to copy my irreverant tone exactly in your own Markdowns. It’s a little window into my psyche. Enjoy =)
hint: go to the PhD Comics website to see if you can find the image above
If you can’t find that exact image, just find a comparable image from the PhD Comics website and include it in your markdown
Let’s be honest, this header is a little arbitrary. But show me that you can reproduce headers with different levels please. This is a level 3 header, for your reference (you can most easily tell this from the table of contents).
Perhaps you’re already really confused by the whole markdown thing. Maybe you’re so confused that you’ve forgotton how to add. Never fear! A calculator R is here:
1231521+12341556280987
## [1] 1.234156e+13
Or maybe, after you’ve added those numbers, you feel like it’s about time for a table! I’m going to leave all the guts of the coding here so you can see how libraries (R packages) are loaded into R (more on that later). It’s not terribly pretty, but it hints at how R works and how you will use it in the future. The summary function used below is a nice data exploration function that you may use in the future.
library(knitr)
kable(summary(cars),caption="I made this table with kable in the knitr package library")
| speed | dist | |
|---|---|---|
| Min. : 4.0 | Min. : 2.00 | |
| 1st Qu.:12.0 | 1st Qu.: 26.00 | |
| Median :15.0 | Median : 36.00 | |
| Mean :15.4 | Mean : 42.98 | |
| 3rd Qu.:19.0 | 3rd Qu.: 56.00 | |
| Max. :25.0 | Max. :120.00 |
And now you’ve almost finished your first RMarkdown! Feeling excited? We are! In fact, we’re so excited that maybe we need a big finale eh? Here’s ours! Include a fun gif of your choice!